Apologies for the delay.
I would expect the results to be slightly different. The accuracy in MachUp is dependent on accurately defining your airfoil properties. Make sure you have defined the airfoil coefficients (aL0, CL,a, CD0, CD,L, CD,L2, etc.) correctly. We have a series of 3 videos that walk you through the process on our site:
http://aero.go.usu.edu/lessons/1-6-airfoil-definition-and-analysis/